Digital Photography - Software
iView Media. I use the 'pro' version to manage my photos, videos and anything else that falls under the term media. Really easy to use and effective image manipulation too. Now owned by Microsoft and being relaunched under the "Expression Media" title; I've not 'upgraded' to this new version because I don't like the integration of things like WMA as a standard, and will be looking for iPhoto to step up and do the job in the future.
Doubletake. Shareware panorama stitching program. Amazingly easy to use and versions available for OS X 10.3.9 and 10.4.x. Best $12 I ever spent on a stitching package!
Calico and PTMac. More panorama stitching packages. I don't use these as are more expensive and I have doubletake. If you do a lot of complex stitching then these may have more options.
For image resizing try Resize, SmallImage or PhotoToolCM.
Apple OSX additions
SMARTReporter . Check your hard drive for problems.
Convert Apple's mail emix files to a more standard mbox format.
Cleardock is a nice little application that removes the white background from beneath your dock, lets you change the colour if you so with a quite possibly some other little tricks.
CeePeeYou adds a CPU usage value to the menu bar.
Looking for a Windows Media Player now that Microsoft are no longer developing their player for the Mac? Try Flip4Mac, an add-on for Quicktime that enables WMV playback and works within a web browser too.
Macjournal is an OSX journaling package that has grown substantially recently to include blogging and applescript support. If you want a simpler, free, version then get version 2.6.1. If you can't get enough of Macjournal then follow the development in Dan Schimpf's blog.
Fugu is a pretty GUI for Secure File Transfer which also supports secure copy. Fugu doesn't support ordinary FTP transfers so you might like to use GSFTP or FTPeel instead.
I've just discovered Cyberduck a FTP and SFTP browser that is available under the GPL. I like it so far and think this will become my file transfer client of choice.
SkypeMenuX adds Skype control back to the menu bar (you know, like it used to be before this functionality was removed!) Means you don't have to bring up he Skype window every time you step away from your computer.
Web
Firefox
Camino
Flock
Opera
Graphical Stuff
ImageMagick.
Color Oracle lets see how your screen (so web page, map, figure... whatever) looks to people with colour blindness of three types. Their links page points to a number of other useful references for colour blindness and choosing colours with a good contrast.
DVD Backup and Transfer to Portable Devices
MediaFork is an open source (available under the GPL) DVD to MPEG-4 ripper/converter. This is an evolution of the software "HandBrake"; if you like you can read more. MediaFork has now been re-merged with HandBrake, so follow that for the latest version.
DVD2oneX
ffmpegX
MacTheRipper
Toast
Utilities
Coconut Battery tells you the state of your battery; not only is current charge shown but the maximum capacity compared with original capacity and information about age and loadcycles. Intel and PPC, and a widget is available!.
And some iPod/iTunes utilities
Copy files back off your ipod with Senuti or possibly even better iPodDisk.
Download underground/tube/subway maps for your ipod with iSubwayMaps.
Install linux on your ipod. This is a non-destructive install, apparently.
Download wikipedia to your iPod with encyclopodia.
iTunesShut will let you play some music as you go to sleep and then shut down your computer if you so wish.
Scientific computing, particularly for OS X
Generic Mapping Tools (GMT). You need this. Follow the instructions for installing this on OSX here.
Fink is a fantastic resource of precompiled packages for scientific (and other computing). This should be the first thing you get, at least after installing X Windows, as it will make everything else easier and quicker.
Wide-angle velocity modeling
Rayinvr a 2-D ray tracing package and v2c a way of converting a simple column orientated velocity model into the rayinvr format and back.